Incidental Mutation 'R7167:Stag1'
ID 557995
Institutional Source Beutler Lab
Gene Symbol Stag1
Ensembl Gene ENSMUSG00000037286
Gene Name STAG1 cohesin complex component
Synonyms SA-1, Scc3
MMRRC Submission 045228-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7167 (G1)
Quality Score 225.009
Status Validated
Chromosome 9
Chromosomal Location 100479762-100840597 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to G at 100827942 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Lysine at position 990 (N990K)
Ref Sequence ENSEMBL: ENSMUSP00000116205 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000041418] [ENSMUST00000123302] [ENSMUST00000129269] [ENSMUST00000155108]
AlphaFold Q9D3E6
Predicted Effect probably benign
Transcript: ENSMUST00000041418
AA Change: N990K

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000040724
Gene: ENSMUSG00000037286
AA Change: N990K

DomainStartEndE-ValueType
low complexity region 32 44 N/A INTRINSIC
low complexity region 59 72 N/A INTRINSIC
Pfam:STAG 157 276 1.5e-50 PFAM
SCOP:d1qbkb_ 279 850 4e-5 SMART
low complexity region 1062 1081 N/A INTRINSIC
low complexity region 1107 1120 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000123302
SMART Domains Protein: ENSMUSP00000117879
Gene: ENSMUSG00000037286

DomainStartEndE-ValueType
low complexity region 32 44 N/A INTRINSIC
low complexity region 59 72 N/A INTRINSIC
Pfam:STAG 157 276 2.9e-51 PFAM
low complexity region 303 315 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000129269
AA Change: N990K

PolyPhen 2 Score 0.050 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000116205
Gene: ENSMUSG00000037286
AA Change: N990K

DomainStartEndE-ValueType
low complexity region 32 44 N/A INTRINSIC
low complexity region 59 72 N/A INTRINSIC
Pfam:STAG 160 274 3.8e-41 PFAM
SCOP:d1qbkb_ 279 850 3e-5 SMART
low complexity region 1062 1081 N/A INTRINSIC
low complexity region 1107 1120 N/A INTRINSIC
Predicted Effect
SMART Domains Protein: ENSMUSP00000115460
Gene: ENSMUSG00000037286
AA Change: N159K

DomainStartEndE-ValueType
low complexity region 232 251 N/A INTRINSIC
Predicted Effect
SMART Domains Protein: ENSMUSP00000120974
Gene: ENSMUSG00000037286
AA Change: N600K

DomainStartEndE-ValueType
low complexity region 673 692 N/A INTRINSIC
low complexity region 718 731 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000155108
SMART Domains Protein: ENSMUSP00000118952
Gene: ENSMUSG00000037286

DomainStartEndE-ValueType
low complexity region 32 44 N/A INTRINSIC
low complexity region 59 72 N/A INTRINSIC
Meta Mutation Damage Score 0.0697 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency 94% (65/69)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the SCC3 family and is expressed in the nucleus. It encodes a component of cohesin, a multisubunit protein complex that provides sister chromatid cohesion along the length of a chromosome from DNA replication through prophase and prometaphase, after which it is dissociated in preparation for segregation during anaphase. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mouse embryos homozygous for a null mutation show developmental delay and die before birth. Heterozygous animals have shorter lifespan and earlier onset of tumourigenesis. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 68 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A2m T C 6: 121,624,930 (GRCm39) V436A probably benign Het
Abcc5 T C 16: 20,224,251 (GRCm39) T111A possibly damaging Het
Acsbg2 T A 17: 57,164,000 (GRCm39) D203V probably benign Het
Alpk2 G T 18: 65,440,049 (GRCm39) T448K probably benign Het
Arhgef2 A G 3: 88,551,179 (GRCm39) N780S possibly damaging Het
Atxn2l T C 7: 126,098,394 (GRCm39) N252S possibly damaging Het
Bmpr1b A T 3: 141,568,841 (GRCm39) L163Q probably benign Het
Clca3a2 T C 3: 144,803,545 (GRCm39) R100G probably benign Het
Col2a1 A G 15: 97,898,337 (GRCm39) I79T unknown Het
Csmd1 A G 8: 15,976,524 (GRCm39) V2898A probably benign Het
Cux1 G A 5: 136,338,895 (GRCm39) probably null Het
Cyp2u1 A G 3: 131,096,773 (GRCm39) S2P probably benign Het
Daam1 C A 12: 72,035,678 (GRCm39) H958N probably damaging Het
Dnah7a C T 1: 53,542,935 (GRCm39) V2412I probably benign Het
Ergic2 T C 6: 148,108,133 (GRCm39) R2G probably damaging Het
Fat2 T C 11: 55,175,827 (GRCm39) T1629A possibly damaging Het
Ftl1 T A 7: 45,109,202 (GRCm39) probably benign Het
Fut8 T C 12: 77,495,406 (GRCm39) V332A possibly damaging Het
Gm28363 T C 1: 117,655,119 (GRCm39) S113P probably damaging Het
Hfe A T 13: 23,892,052 (GRCm39) V104E probably damaging Het
Ifih1 A T 2: 62,429,240 (GRCm39) N899K probably benign Het
Krt75 A G 15: 101,476,750 (GRCm39) S380P possibly damaging Het
Meiob T G 17: 25,055,419 (GRCm39) F409V probably damaging Het
Mkrn2os A T 6: 115,562,474 (GRCm39) I163N probably damaging Het
Nanos1 G T 19: 60,745,046 (GRCm39) G115W probably damaging Het
Naprt C T 15: 75,764,461 (GRCm39) A276T probably damaging Het
Oas1e G T 5: 120,933,487 (GRCm39) T26N probably benign Het
Oog2 T G 4: 143,921,745 (GRCm39) D218E probably benign Het
Optn T C 2: 5,047,294 (GRCm39) N207S probably benign Het
Or13a20 T A 7: 140,232,466 (GRCm39) C191* probably null Het
Or1l8 T C 2: 36,817,533 (GRCm39) I198V probably benign Het
Or4g16 T C 2: 111,136,793 (GRCm39) M81T probably benign Het
Or4p18 A G 2: 88,232,552 (GRCm39) V242A possibly damaging Het
Or6c63-ps1 T G 10: 128,899,141 (GRCm39) Q245P probably damaging Het
Or6c66b T C 10: 129,376,607 (GRCm39) L67P possibly damaging Het
Or8g4 T C 9: 39,661,865 (GRCm39) F61S probably damaging Het
Oxnad1 G T 14: 31,822,976 (GRCm39) E236* probably null Het
Pcdha3 G A 18: 37,080,046 (GRCm39) A263T probably damaging Het
Pex13 A T 11: 23,605,472 (GRCm39) W253R possibly damaging Het
Pip5k1b T A 19: 24,374,433 (GRCm39) E49D probably benign Het
Plau C A 14: 20,889,518 (GRCm39) F194L possibly damaging Het
Ppm1n A G 7: 19,013,666 (GRCm39) L95S probably damaging Het
Pramel40 G A 5: 94,464,984 (GRCm39) A457T possibly damaging Het
Radil G T 5: 142,471,260 (GRCm39) probably null Het
Ralgapa2 C T 2: 146,190,374 (GRCm39) M1266I probably benign Het
Reln A T 5: 22,147,618 (GRCm39) L2444Q probably damaging Het
Rims2 T C 15: 39,300,473 (GRCm39) V260A probably benign Het
Rnase2b T A 14: 51,400,222 (GRCm39) V101E probably damaging Het
Rtp3 T A 9: 110,815,772 (GRCm39) T198S probably benign Het
Shisal2b A G 13: 105,000,166 (GRCm39) V19A probably damaging Het
Smad3 T A 9: 63,573,435 (GRCm39) D201V probably benign Het
Son AGAACCCCCAGCCGCAGGAGCCGAACCCCCAGCCGCAGGAGCCGAACCCCCAGCCGCAGGAGCCGAACCCCCAGCCG AGAACCCCCAGCCGCAGGAGCCGAACCCCCAGCCGCAGGAGCCGAACCCCCAGCCG 16: 91,457,222 (GRCm39) probably benign Het
Spata7 T G 12: 98,630,555 (GRCm39) F371C probably damaging Het
Tbx18 C T 9: 87,589,883 (GRCm39) A352T probably damaging Het
Thada C T 17: 84,538,391 (GRCm39) R1539Q probably benign Het
Thrap3 A C 4: 126,078,920 (GRCm39) probably benign Het
Tnks G A 8: 35,316,458 (GRCm39) T887M probably damaging Het
Trap1 A C 16: 3,870,792 (GRCm39) V393G probably damaging Het
Trpm4 A G 7: 44,977,143 (GRCm39) probably null Het
Trrap G T 5: 144,776,424 (GRCm39) G3007C probably benign Het
U2surp A T 9: 95,363,726 (GRCm39) N611K probably damaging Het
Usp12 A G 5: 146,705,745 (GRCm39) probably null Het
Vmn1r200 A G 13: 22,579,487 (GRCm39) T97A possibly damaging Het
Vmn2r110 C T 17: 20,794,441 (GRCm39) V743I probably benign Het
Vps50 C T 6: 3,600,256 (GRCm39) T905M probably damaging Het
Wdr48 T A 9: 119,736,855 (GRCm39) probably null Het
Zfp446 C T 7: 12,712,049 (GRCm39) probably benign Het
Zfr T C 15: 12,181,015 (GRCm39) S1012P probably benign Het
Other mutations in Stag1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00649:Stag1 APN 9 100,658,861 (GRCm39) missense probably damaging 1.00
IGL01010:Stag1 APN 9 100,827,986 (GRCm39) missense probably benign 0.06
IGL01012:Stag1 APN 9 100,737,912 (GRCm39) missense possibly damaging 0.47
IGL01025:Stag1 APN 9 100,833,710 (GRCm39) missense possibly damaging 0.95
IGL01307:Stag1 APN 9 100,833,841 (GRCm39) intron probably benign
IGL02149:Stag1 APN 9 100,769,442 (GRCm39) missense probably benign 0.09
IGL02608:Stag1 APN 9 100,639,822 (GRCm39) missense probably null 0.99
IGL03008:Stag1 APN 9 100,658,844 (GRCm39) missense probably damaging 1.00
IGL03210:Stag1 APN 9 100,727,129 (GRCm39) missense possibly damaging 0.63
eto_o UTSW 9 100,678,769 (GRCm39) missense probably damaging 1.00
PIT4280001:Stag1 UTSW 9 100,824,769 (GRCm39) missense possibly damaging 0.95
R0070:Stag1 UTSW 9 100,838,461 (GRCm39) missense probably null 1.00
R0070:Stag1 UTSW 9 100,838,461 (GRCm39) missense probably null 1.00
R0349:Stag1 UTSW 9 100,658,837 (GRCm39) missense probably damaging 0.98
R0479:Stag1 UTSW 9 100,810,144 (GRCm39) missense probably benign 0.00
R0531:Stag1 UTSW 9 100,836,300 (GRCm39) makesense probably null
R0962:Stag1 UTSW 9 100,678,880 (GRCm39) missense probably damaging 1.00
R0976:Stag1 UTSW 9 100,812,069 (GRCm39) critical splice donor site probably null
R0976:Stag1 UTSW 9 100,658,877 (GRCm39) missense probably damaging 0.98
R1170:Stag1 UTSW 9 100,770,506 (GRCm39) intron probably benign
R1499:Stag1 UTSW 9 100,769,426 (GRCm39) intron probably benign
R1499:Stag1 UTSW 9 100,737,885 (GRCm39) missense possibly damaging 0.77
R1644:Stag1 UTSW 9 100,762,953 (GRCm39) intron probably benign
R1747:Stag1 UTSW 9 100,770,353 (GRCm39) missense probably benign
R1799:Stag1 UTSW 9 100,835,515 (GRCm39) splice site probably null
R1807:Stag1 UTSW 9 100,790,719 (GRCm39) missense probably benign 0.34
R1978:Stag1 UTSW 9 100,770,139 (GRCm39) missense probably benign 0.03
R2029:Stag1 UTSW 9 100,668,740 (GRCm39) missense probably damaging 1.00
R2161:Stag1 UTSW 9 100,771,648 (GRCm39) missense probably damaging 1.00
R2300:Stag1 UTSW 9 100,594,553 (GRCm39) missense possibly damaging 0.92
R2327:Stag1 UTSW 9 100,668,666 (GRCm39) missense possibly damaging 0.81
R2426:Stag1 UTSW 9 100,727,169 (GRCm39) critical splice donor site probably null
R2448:Stag1 UTSW 9 100,770,462 (GRCm39) missense probably benign 0.42
R2504:Stag1 UTSW 9 100,748,263 (GRCm39) missense probably damaging 0.99
R3713:Stag1 UTSW 9 100,771,671 (GRCm39) missense probably benign 0.01
R3835:Stag1 UTSW 9 100,620,035 (GRCm39) missense probably damaging 0.97
R3862:Stag1 UTSW 9 100,826,838 (GRCm39) missense probably benign 0.02
R4398:Stag1 UTSW 9 100,838,659 (GRCm39) utr 3 prime probably benign
R4568:Stag1 UTSW 9 100,730,722 (GRCm39) missense probably damaging 1.00
R4651:Stag1 UTSW 9 100,678,769 (GRCm39) missense probably damaging 1.00
R4652:Stag1 UTSW 9 100,678,769 (GRCm39) missense probably damaging 1.00
R4653:Stag1 UTSW 9 100,678,769 (GRCm39) missense probably damaging 1.00
R4675:Stag1 UTSW 9 100,730,758 (GRCm39) missense probably damaging 1.00
R4709:Stag1 UTSW 9 100,620,092 (GRCm39) missense probably damaging 0.99
R4924:Stag1 UTSW 9 100,678,808 (GRCm39) missense possibly damaging 0.67
R5018:Stag1 UTSW 9 100,833,672 (GRCm39) missense probably benign 0.00
R5435:Stag1 UTSW 9 100,835,603 (GRCm39) missense probably benign 0.03
R5460:Stag1 UTSW 9 100,838,506 (GRCm39) splice site probably null
R5805:Stag1 UTSW 9 100,678,831 (GRCm39) missense probably damaging 1.00
R6127:Stag1 UTSW 9 100,833,750 (GRCm39) missense probably benign 0.05
R6313:Stag1 UTSW 9 100,639,786 (GRCm39) missense probably damaging 1.00
R6597:Stag1 UTSW 9 100,769,473 (GRCm39) missense probably benign 0.01
R6807:Stag1 UTSW 9 100,826,903 (GRCm39) missense probably damaging 1.00
R7099:Stag1 UTSW 9 100,826,879 (GRCm39) missense probably benign 0.02
R7395:Stag1 UTSW 9 100,678,781 (GRCm39) missense probably damaging 0.99
R7504:Stag1 UTSW 9 100,770,381 (GRCm39) missense probably benign 0.09
R7663:Stag1 UTSW 9 100,620,191 (GRCm39) missense probably damaging 0.98
R7769:Stag1 UTSW 9 100,826,880 (GRCm39) missense possibly damaging 0.86
R8245:Stag1 UTSW 9 100,811,946 (GRCm39) missense probably benign 0.01
R8343:Stag1 UTSW 9 100,639,819 (GRCm39) missense possibly damaging 0.95
R8473:Stag1 UTSW 9 100,762,840 (GRCm39) missense probably damaging 1.00
R8709:Stag1 UTSW 9 100,772,975 (GRCm39) intron probably benign
R8925:Stag1 UTSW 9 100,587,298 (GRCm39) missense possibly damaging 0.46
R8927:Stag1 UTSW 9 100,587,298 (GRCm39) missense possibly damaging 0.46
R8951:Stag1 UTSW 9 100,762,854 (GRCm39) missense probably damaging 1.00
R9138:Stag1 UTSW 9 100,829,335 (GRCm39) missense probably benign 0.01
R9233:Stag1 UTSW 9 100,812,024 (GRCm39) missense probably benign 0.00
R9246:Stag1 UTSW 9 100,770,329 (GRCm39) missense probably benign 0.00
R9419:Stag1 UTSW 9 100,811,967 (GRCm39) missense probably benign
R9442:Stag1 UTSW 9 100,836,306 (GRCm39) missense probably damaging 1.00
R9694:Stag1 UTSW 9 100,810,151 (GRCm39) missense probably benign 0.05
R9740:Stag1 UTSW 9 100,587,288 (GRCm39) missense probably damaging 0.98
Predicted Primers PCR Primer
(F):5'- TCCAAGGATTTGTATTACCCCTG -3'
(R):5'- ATAGCTTCCAGGTCAAACCAAG -3'

Sequencing Primer
(F):5'- TACCCCTGAAAAATACATTGGGG -3'
(R):5'- CCAGGTCAAACCAAGTTTTTATTAC -3'
Posted On 2019-06-26